In the game, Mages have always existed, though there are legends of the Pure Ones who were shards of the original, divine One. Early mages cultivated their magical beliefs alone or in small groups, generally conforming to and influencing the belief systems of their societies. Obscure myths suggest that the precursors of the modern organizations of mages originally gathered in ancient Egypt. This period of historical uncertainty also saw the rise of the Nephandi in the Near East. This set the stage for what the game's history calls the Mythic Ages.
Until the late Middle Ages, mages' fortunes waxed and waned along with their native societies. Eventually, though, mages belonging to the Order of Hermes and the Messianic Voices attained great influence over European society. However, absorbed by their pursuit of occult power and esoteric knowledge, they often neglected and even abused humanity. Frequently, they were at odds with mainstream religions, envied by noble authorities and cursed by common folk.
Seeing their chance, mages who believed in proto-scientific theories banded together under the banner of the Order of Reason, declaring their aim was to create a safe world with Man as its ruler. They won the support of Sleepers by developing the useful arts of manufacturing, economy, wayfaring and medicine. They also championed many of the values that we now associate with the Renaissance. Masses of Sleepers embraced the gifts of early Technology and the Science that accompanied them. As the masses' beliefs shifted, the Consensus changed and wizards began to lose their position as their power and influence waned.
This was intentional. The Order of Reason perceived a safe world as one devoid of heretical beliefs, ungodly practices and supernatural creatures preying upon humanity. As the defenders of the common folk, they intended to replace the dominant magical groups with a society of philosopher-scientists as shepherds, protecting and guiding humanity. In response, non-scientific mages banded together to form the Council of Nine Traditions where mages of all the major magical paths gathered. They fought on battlefields and in universities trying to undermine as many discoveries as they could, but to no avail - technology made the march of Science unstoppable. The Traditions' power bases were crippled, their believers mainly converted, their beliefs ridiculed all around the world. Their final counteroffensives against the Order of Reason were foiled by internal dissent and treachery in their midst.
However, from the turn of 17th century on, the goals of the Order of Reason began to change. As their scientific paradigm unfolded, they decided that the mystical beliefs of the common people were not only backward, but dangerous, and that they should be replaced by cold, measurable and predictable laws of nature and respect for human genius. They replaced long-held theologies, pantheons, and mystical traditions with ideas like rational thought and the scientific method. As more and more sleepers began to use the Order's discoveries in their everyday lives, Reason and rationality came to govern their beliefs, and the old ways came to be regarded as misguided superstition. However, The Order of Reason became less and less focused on improving the daily lives of sleepers and more concerned with eliminating any resistance to their choke hold on the minds of humanity. Ever since a reorganization performed under Queen Victoria in the late 1800s, they call themselves The Technocracy.
The Order of Reason renamed itself the Technocracy and espoused an authoritarian rule over Sleepers' beliefs, while suppressing the Council of Nine's attempts to reintroduce magic. The Traditions replenished their numbers (which had been diminished by the withdrawal of two Traditions, the secretive Ahl-i-Batin, and the Solificati, alchemists plagued by scandal) with former Technocrats from the Sons of Ether and Virtual Adepts factions, vying for the beliefs of sleepers and with the Technocracy, and perpetually wary of the Nephandi (mages who consciously embrace evil and service to a demonic or alien master) and the Marauders (mages who resist Paradox with a magical form of madness). While the Technocracy's propaganda campaigns were effective in turning the Consensus against mystic and heterodox science, the Traditions maintained various resources, including magical nodes, hidden schools and fortresses called Chantries, and various realms outside of the Consensus in the Umbra.
Finally, from 1997-2000, a series of metaplot events destroyed the Council of Nine's Umbral steadings, killing many of their most powerful members. This also cut the Technocracy off from their leadership. Both sides called a truce in their struggle to assess their new situation, especially since these events implied that Armageddon was soon at hand. Chief among these signs was creation of a barrier between the physical world and spirit world (the Umbra). This barrier was called the Avatar Storm because it affected the spiritual being of the Mage (the Avatar). This Avatar Storm was the result of a battle in India on the so-called "Week of Nightmares."
These changes were introduced in supplements for the second edition of the game and became core material in the third edition.
Aside from common changes introduced by the World of Darkness metaplot, mages dealt with renewed conflict when the hidden Rogue Council and the Technocracy's Panopticon encouraged the Traditions and Technocracy to struggle once again. The Rogue Council only made itself known through coded missives, while Panopticon was apparently created by the leaders of the Technocracy to counter it.
This struggle eventually led to the point on the timeline occupied by the book called Ascension. While the entire metaplot has always been meant to be altered as each play group sees fit, Ascension provided multiple possible endings, with none of them being definitive (though one was meant to resolve the metaplot). Thus, there is no definitive canonical ending. Since the game is meant to be adapted to a group's tastes, the importance of this and the preceding storyline is largely a matter of personal preference.